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6 protocols using ab16667

1

Immunohistochemistry of Cell Markers

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Immunohistochemistry was completed on 12 µm frozen sections prepared as above. Antigen retrieval was performed by placing slides in 1% SDS for 5 min. Slides were treated for endogenous peroxidase activity by incubating in 3% H2O2 for 10 min. Blocking was performed in 1% goat serum. The following primary antibodies were used: Ki67 (Abcam ab16667, 1:50), CD44 (Santa Cruz sc-18849, 1:100) and P75 (Abcam ab71822, 1:100). After overnight incubation at 4°C, slides were washed in TBS and incubated with species-appropriate biotinylated secondary antibody (1:200) at room temperature for 1 hr. Finally slides were incubated for 1 hr with Streptavidin Alexa 647 (Molecular Probes S21374, 1:200) and mounted with DAPI containing medium.
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2

Immunohistochemical Analysis of Tumor Markers

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The tumor tissues were fixed in 10% neutral-buffered paraformaldehyde, followed by immersion in liquid paraffin, and sectioned (5-μm thickness). Then, the samples were stained with hematoxylin and eosin and with antibodies against Ki-67 (Abcam, ab16667), NF-κB p65 (Santa Cruz, sc514451), p-IκBα (Santa Cruz, sc8404), p21 (Proteintech, #10355-1-AP), CDK4 (Epitomics, #3830-1), CDK6 (Proteintech, #14052-1-AP), CDK2 (Abcam ab32147), p-Rb (Ser807, Abcam, ab184796), E2F1 (St John’s Laboratory, STJ92807), Skp2 (Santa Cruz, sc7164), c-MYC (Abcam, ab32072), and p27 (sc528, Santa Cruz). Finally, the sections were mounted with DPX Mountant (Sigma, 317616) for histological analysis. Staining scores were noted by the intensity and percentage of positively stained cells. The percentage of positive tumor cells was divided into four grades: 0 (<5% positive), 1 (<25% positive), 2 (25–50% positive), 3 for (51–75% positive), and 4 (>75% positive). The intensity of immunostaining was scored as follows: 0 (no staining), 1 (weak staining), 2 (intermediate staining), or 3 (strong staining). Ten random fields were selected and viewed at ×400 in each section to obtain an average score (Li et al., 2020 (link)).
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3

Immunofluorescence Staining of Muscle Tissue

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Muscle sections attached to positively charged frosted glass microscope slides were fixed with 70% ethanol at 4 °C overnight and rinsed with 1× phosphate-buffered saline (PBS) the next day. The sections were then blocked for 30 min in 1% staining buffer (1% calf serum in 1× PBS). Samples were permeabilized with 0.1% Triton X-100 in 1X PBS for 5 min at room temperature and subsequently rinsed with 1% staining buffer 3 times, 5 min per rinse. The sections were incubated with primary antibodies diluted to 0.5–1 μg/ml at 4 °C overnight. The slides were rinsed as stated and then coated with secondary antibodies and Hoechst nuclear DNA stain for 2 h at room temperature in the dark. Samples were rinsed with PBS and mounted with Fluoromount. A Zeiss Axioscope fluorescent microscope was used for imaging. antibodies: rabbit anti-GFP antibody (abcam290,1:5000), rabbit anti-Ki67(ab16667, 1:200), and mouse anti-dystrophin antibody (Santa Cruz Biotechnology 58754,1:200) were used at dilutions according to manufacturer’s instructions. Secondary fluorochrome conjugated antibodies were from Life Technologies: goat anti-rabbit 546 (A11010, 1:2000) and goat anti-mouse 488 (A11029, 1:2000). DNA was stained by Hoechst 33342 from Sigma Aldrich (B2261) 1:500 at 1 μg/mL.
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4

Immunofluorescence Staining of Organoids

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Organoids were cultured in 4-well chamber slides (BD Biosciences), fixed in 4% PFA for 30 min, washed with PBS + 4% NaCl and blocked and permeabilized in blocking buffer (5% FBS, 0.2% BSA, 0.3% Triton X-100 in PBS) for 30 min. The following primary antibodies were applied at 4 °C overnight in blocking buffer: rat anti-vimentin (MAB2105, R&D Systems), rabbit anti-lumican (ab168348, Abcam), rabbit anti-active caspase-3 (AF835, R&D Systems), rabbit anti-Ki67 (Abcam, ab16667), rabbit anti-mucin2 (Santa-Cruz Biotechnology, sc-15334). After washing in PBS containing 0.3% Triton X-100 and 4% NaCl and overnight incubation with the secondary antibodies (Alexa Fluor 488 and 594, Thermo Fisher), the organoids were mounted in mounting medium containing DAPI (Thermo Fisher) and imaged with an Olympus FV500 confocal microscope.
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5

Histological Evaluation of Glioma Samples

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Tumor samples fixed in 10% formalin were embedded in paraffin by the Duke Pathology Core and cut into 5-μm–thick sections using a Leica RM2235 microtome. Hematoxylin and eosin (H&E) staining was performed using standard protocols. Tumor grading was done using the following criteria: low-grade glioma (grade II) was indicated by an increased cellular density and the presence of Ki67 + cells; high-grade glioma (grades III and IV) was indicated by the presence of microvascular proliferation and/or the presence of pseudopalisading necrosis. Immunohistochemistry (IHC) was performed using an automated processor (Discovery XT, Ventana Medical Systems, Inc.). Antibodies used were anti-Olig2 (Millipore, #AB9610, 1:500), anti-GFAP (Dako, #Z0334, 1:2,000), anti-Nestin (BD Pharmingen, #556309, 1:200), anti-Ki67 (Abcam #ab16667, 1:200), anti-HA (Santa Cruz Biotechnology, #SC-805, 1:250), and anti–Tri-Methyl-Histone H3 Lys27 (Cell Signaling, #C36B11, 1:200). For rabbit antibodies, 10% normal goat serum in 2% BSA was used for the option/blocking step, and biotinylated goat anti-rabbit IgG (Vector Laboratories, #BA-1000, 1:300) was used for detection. For mouse antibodies, the Mouse on Mouse Basic Kit (Mouse on Mouse, Vector Laboratories, #BMK-2202) was used as directed for the option/blocking and detection steps.
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6

Immunohistochemical Analysis of Protein Markers

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Tissue was fixed in buffered 10% formalin overnight; transferred to 70% ethanol and then sectioned, processed and embedded in paraffin. Target antigen retrieval solution at pH 6 (Dako, Carpinteria, CA, USA) was used for antigen retrieval and all slides were treated with 3% H2O2 in methanol to block endogenous peroxidases. General protein blocking was performed with serum-free blocking solution (Dako, Carpenteria, CA, USA). The slides were stained with antibodies against Ki-67 (Abcam, ab16667), ERα (Santa Cruz, 2Q418) or γ-H2A.X (phospho S139, Abcam, ab26350). The secondary antibodies used were biotinylated goat anti-rabbit IgG (Vector Laboratories, Burlingame, CA, USA; BA-100) for Ki-67, biotinylated goat anti-mouse IgG (Abcam, Cambridge, MA, USA; ab64255) for ERα and γ-H2A.X. All slides were counterstained with hematoxylin and imaged on a Leica CTR5000 microscope (Wetzlar, Germany). Quantification was done on triplicate photomicrographs (depicted as panels in images) by counting positively stained cells by a blinded investigator. Images that are representative of organs from 3 animals are shown in figures. Blinded, non-quantitative histological evaluation of mammary tumors was performed by a pathologist [G.K.M.]
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